Starting phenix.real_space_refine on Sat Dec 9 02:18:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kn8_0729/12_2023/6kn8_0729_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kn8_0729/12_2023/6kn8_0729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kn8_0729/12_2023/6kn8_0729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kn8_0729/12_2023/6kn8_0729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kn8_0729/12_2023/6kn8_0729_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kn8_0729/12_2023/6kn8_0729_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 375 5.16 5 C 38106 2.51 5 N 10360 2.21 5 O 12095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 4": "OE1" <-> "OE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 4": "OE1" <-> "OE2" Residue "M PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 4": "OE1" <-> "OE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 286": "OD1" <-> "OD2" Residue "N TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 4": "OE1" <-> "OE2" Residue "O PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 286": "OD1" <-> "OD2" Residue "O TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 60966 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "F" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "H" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "I" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "J" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "K" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "L" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "M" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "N" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "O" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "P" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "Q" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "R" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "S" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "T" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1101 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'TRANS': 125} Chain breaks: 1 Chain: "U" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1009 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "V" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1273 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "W" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "X" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "Y" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "Z" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "a" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1101 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'TRANS': 125} Chain breaks: 1 Chain: "b" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1009 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "c" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1273 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.20, per 1000 atoms: 0.38 Number of scatterers: 60966 At special positions: 0 Unit cell: (130.98, 170.94, 486.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 375 16.00 P 30 15.00 O 12095 8.00 N 10360 7.00 C 38106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.74 Conformation dependent library (CDL) restraints added in 8.4 seconds 15214 Ramachandran restraints generated. 7607 Oldfield, 0 Emsley, 7607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 61 sheets defined 54.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.92 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 137 through 145 removed outlier: 4.057A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.588A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 261 removed outlier: 4.915A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.418A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.847A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.569A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.077A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.124A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.653A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.735A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.770A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 293 No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 350 through 355 removed outlier: 5.267A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.770A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.503A pdb=" N LYS D 118 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR D 120 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 122 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 123 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.500A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.379A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.743A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.350A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.541A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 195 Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 252 through 261 removed outlier: 4.804A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 294 removed outlier: 4.037A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 338 through 347 Processing helix chain 'F' and resid 350 through 355 removed outlier: 5.173A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.657A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 195 Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 287 through 294 removed outlier: 4.179A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 318 Processing helix chain 'G' and resid 338 through 347 Processing helix chain 'G' and resid 350 through 352 No H-bonds generated for 'chain 'G' and resid 350 through 352' Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.728A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 195 removed outlier: 3.565A pdb=" N ASP H 187 " --> pdb=" O ARG H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 252 through 256 Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 287 through 294 removed outlier: 4.506A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 318 removed outlier: 3.567A pdb=" N GLN H 314 " --> pdb=" O ALA H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 347 Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.724A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 137 through 145 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 195 Processing helix chain 'I' and resid 203 through 216 Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 252 through 261 removed outlier: 5.047A pdb=" N CYS I 257 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 274 through 283 Processing helix chain 'I' and resid 287 through 294 removed outlier: 3.924A pdb=" N LYS I 291 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 338 through 347 Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 361 through 365 Processing helix chain 'I' and resid 367 through 373 removed outlier: 3.689A pdb=" N LYS I 373 " --> pdb=" O VAL I 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 92 Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 114 through 125 Processing helix chain 'J' and resid 137 through 145 Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 203 through 216 Processing helix chain 'J' and resid 223 through 230 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 252 through 261 removed outlier: 3.512A pdb=" N ARG J 256 " --> pdb=" O GLU J 253 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N CYS J 257 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Proline residue: J 258 - end of helix Processing helix chain 'J' and resid 264 through 267 Processing helix chain 'J' and resid 274 through 283 Processing helix chain 'J' and resid 290 through 296 Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 338 through 347 Processing helix chain 'J' and resid 350 through 352 No H-bonds generated for 'chain 'J' and resid 350 through 352' Processing helix chain 'J' and resid 361 through 365 Processing helix chain 'J' and resid 367 through 373 removed outlier: 3.730A pdb=" N LYS J 373 " --> pdb=" O VAL J 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 79 through 92 Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 113 through 125 Processing helix chain 'K' and resid 137 through 145 Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 182 through 195 removed outlier: 3.537A pdb=" N ASP K 187 " --> pdb=" O ARG K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 216 Processing helix chain 'K' and resid 223 through 230 Processing helix chain 'K' and resid 234 through 236 No H-bonds generated for 'chain 'K' and resid 234 through 236' Processing helix chain 'K' and resid 252 through 256 Processing helix chain 'K' and resid 258 through 261 Processing helix chain 'K' and resid 264 through 267 Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 287 through 293 removed outlier: 3.908A pdb=" N ARG K 290 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS K 291 " --> pdb=" O ASP K 288 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP K 292 " --> pdb=" O ILE K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 320 Processing helix chain 'K' and resid 338 through 347 Processing helix chain 'K' and resid 350 through 352 No H-bonds generated for 'chain 'K' and resid 350 through 352' Processing helix chain 'K' and resid 359 through 365 Processing helix chain 'K' and resid 367 through 373 removed outlier: 3.766A pdb=" N LYS K 373 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 145 Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 182 through 195 removed outlier: 3.520A pdb=" N ASP L 187 " --> pdb=" O ARG L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 Processing helix chain 'L' and resid 223 through 230 Processing helix chain 'L' and resid 234 through 236 No H-bonds generated for 'chain 'L' and resid 234 through 236' Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.800A pdb=" N CYS L 257 " --> pdb=" O ARG L 254 " (cutoff:3.500A) Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 274 through 283 Processing helix chain 'L' and resid 287 through 294 removed outlier: 4.093A pdb=" N LYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 309 through 318 Processing helix chain 'L' and resid 338 through 348 Processing helix chain 'L' and resid 350 through 355 removed outlier: 5.285A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 365 Processing helix chain 'L' and resid 367 through 373 removed outlier: 3.775A pdb=" N LYS L 373 " --> pdb=" O VAL L 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 98 through 100 No H-bonds generated for 'chain 'M' and resid 98 through 100' Processing helix chain 'M' and resid 113 through 125 Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 182 through 195 Processing helix chain 'M' and resid 203 through 216 Processing helix chain 'M' and resid 223 through 230 Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 252 through 262 removed outlier: 4.871A pdb=" N CYS M 257 " --> pdb=" O ARG M 254 " (cutoff:3.500A) Proline residue: M 258 - end of helix Processing helix chain 'M' and resid 264 through 267 Processing helix chain 'M' and resid 274 through 283 Processing helix chain 'M' and resid 287 through 296 removed outlier: 5.291A pdb=" N ASP M 292 " --> pdb=" O ASP M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 318 Processing helix chain 'M' and resid 338 through 347 Processing helix chain 'M' and resid 350 through 354 removed outlier: 3.633A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 365 Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.575A pdb=" N VAL M 370 " --> pdb=" O PRO M 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 60 Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 79 through 90 Processing helix chain 'N' and resid 98 through 100 No H-bonds generated for 'chain 'N' and resid 98 through 100' Processing helix chain 'N' and resid 113 through 125 Processing helix chain 'N' and resid 137 through 145 Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 182 through 195 Processing helix chain 'N' and resid 203 through 216 Processing helix chain 'N' and resid 223 through 230 Processing helix chain 'N' and resid 234 through 236 No H-bonds generated for 'chain 'N' and resid 234 through 236' Processing helix chain 'N' and resid 252 through 262 removed outlier: 4.824A pdb=" N CYS N 257 " --> pdb=" O ARG N 254 " (cutoff:3.500A) Proline residue: N 258 - end of helix Processing helix chain 'N' and resid 264 through 267 Processing helix chain 'N' and resid 274 through 283 Processing helix chain 'N' and resid 287 through 296 removed outlier: 3.846A pdb=" N LYS N 291 " --> pdb=" O ILE N 287 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP N 292 " --> pdb=" O ASP N 288 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA N 295 " --> pdb=" O LYS N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 318 Processing helix chain 'N' and resid 338 through 347 Processing helix chain 'N' and resid 350 through 352 No H-bonds generated for 'chain 'N' and resid 350 through 352' Processing helix chain 'N' and resid 361 through 365 Processing helix chain 'N' and resid 367 through 373 removed outlier: 3.584A pdb=" N LYS N 373 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 60 Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'O' and resid 79 through 92 Processing helix chain 'O' and resid 98 through 100 No H-bonds generated for 'chain 'O' and resid 98 through 100' Processing helix chain 'O' and resid 113 through 125 Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.762A pdb=" N SER O 141 " --> pdb=" O GLN O 137 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 182 through 195 Processing helix chain 'O' and resid 203 through 216 Processing helix chain 'O' and resid 223 through 230 Processing helix chain 'O' and resid 234 through 236 No H-bonds generated for 'chain 'O' and resid 234 through 236' Processing helix chain 'O' and resid 252 through 262 removed outlier: 4.865A pdb=" N CYS O 257 " --> pdb=" O ARG O 254 " (cutoff:3.500A) Proline residue: O 258 - end of helix Processing helix chain 'O' and resid 264 through 267 Processing helix chain 'O' and resid 274 through 283 Processing helix chain 'O' and resid 287 through 296 removed outlier: 4.083A pdb=" N LYS O 291 " --> pdb=" O ILE O 287 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASP O 292 " --> pdb=" O ASP O 288 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA O 295 " --> pdb=" O LYS O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 309 through 320 Processing helix chain 'O' and resid 338 through 347 Processing helix chain 'O' and resid 350 through 352 No H-bonds generated for 'chain 'O' and resid 350 through 352' Processing helix chain 'O' and resid 361 through 365 Processing helix chain 'O' and resid 367 through 373 Processing helix chain 'P' and resid 12 through 280 Processing helix chain 'Q' and resid 14 through 281 removed outlier: 3.925A pdb=" N ALA Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 27 Processing helix chain 'S' and resid 2 through 28 Processing helix chain 'T' and resid 100 through 148 Processing helix chain 'T' and resid 200 through 214 Processing helix chain 'T' and resid 226 through 270 Processing helix chain 'U' and resid 43 through 79 Processing helix chain 'U' and resid 90 through 135 Processing helix chain 'U' and resid 151 through 162 removed outlier: 7.788A pdb=" N ALA U 161 " --> pdb=" O ALA U 157 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ARG U 162 " --> pdb=" O LEU U 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 14 through 27 Processing helix chain 'V' and resid 38 through 47 Processing helix chain 'V' and resid 54 through 62 Processing helix chain 'V' and resid 74 through 83 Processing helix chain 'V' and resid 94 through 104 removed outlier: 3.636A pdb=" N MET V 103 " --> pdb=" O ASP V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 124 removed outlier: 3.572A pdb=" N THR V 124 " --> pdb=" O MET V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 140 Processing helix chain 'V' and resid 150 through 156 Processing helix chain 'W' and resid 12 through 280 Processing helix chain 'X' and resid 14 through 281 removed outlier: 3.924A pdb=" N ALA X 269 " --> pdb=" O LEU X 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 27 Processing helix chain 'Z' and resid 2 through 28 Processing helix chain 'a' and resid 100 through 148 Processing helix chain 'a' and resid 200 through 214 Processing helix chain 'a' and resid 226 through 270 Processing helix chain 'b' and resid 43 through 79 Processing helix chain 'b' and resid 90 through 135 Processing helix chain 'b' and resid 151 through 162 removed outlier: 7.789A pdb=" N ALA b 161 " --> pdb=" O ALA b 157 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ARG b 162 " --> pdb=" O LEU b 158 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 10 Processing helix chain 'c' and resid 14 through 27 Processing helix chain 'c' and resid 38 through 47 Processing helix chain 'c' and resid 54 through 62 Processing helix chain 'c' and resid 74 through 83 Processing helix chain 'c' and resid 94 through 104 removed outlier: 3.636A pdb=" N MET c 103 " --> pdb=" O ASP c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 124 removed outlier: 3.572A pdb=" N THR c 124 " --> pdb=" O MET c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 140 Processing helix chain 'c' and resid 150 through 156 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.717A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.710A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 163 through 165 Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= L, first strand: chain 'C' and resid 163 through 165 Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= N, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.705A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= P, first strand: chain 'D' and resid 163 through 165 Processing sheet with id= Q, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= R, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.519A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= T, first strand: chain 'E' and resid 163 through 165 Processing sheet with id= U, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= V, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.636A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= X, first strand: chain 'F' and resid 163 through 165 Processing sheet with id= Y, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Z, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.557A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 34 through 38 Processing sheet with id= AB, first strand: chain 'G' and resid 163 through 165 Processing sheet with id= AC, first strand: chain 'G' and resid 238 through 241 Processing sheet with id= AD, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.485A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 34 through 38 Processing sheet with id= AF, first strand: chain 'H' and resid 163 through 165 Processing sheet with id= AG, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= AH, first strand: chain 'I' and resid 132 through 135 removed outlier: 6.765A pdb=" N THR I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA I 135 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 34 through 38 Processing sheet with id= AJ, first strand: chain 'I' and resid 163 through 165 Processing sheet with id= AK, first strand: chain 'I' and resid 238 through 241 Processing sheet with id= AL, first strand: chain 'J' and resid 132 through 136 removed outlier: 6.744A pdb=" N THR J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA J 135 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N CYS J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 34 through 38 Processing sheet with id= AN, first strand: chain 'J' and resid 163 through 165 Processing sheet with id= AO, first strand: chain 'J' and resid 238 through 241 Processing sheet with id= AP, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.797A pdb=" N THR K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA K 135 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'K' and resid 34 through 38 Processing sheet with id= AR, first strand: chain 'K' and resid 163 through 165 Processing sheet with id= AS, first strand: chain 'K' and resid 238 through 241 Processing sheet with id= AT, first strand: chain 'L' and resid 132 through 136 removed outlier: 6.814A pdb=" N THR L 103 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA L 135 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU L 105 " --> pdb=" O ALA L 135 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N CYS L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'L' and resid 35 through 38 Processing sheet with id= AV, first strand: chain 'L' and resid 163 through 165 Processing sheet with id= AW, first strand: chain 'L' and resid 238 through 241 Processing sheet with id= AX, first strand: chain 'M' and resid 132 through 136 removed outlier: 6.633A pdb=" N THR M 103 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA M 135 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'M' and resid 34 through 38 Processing sheet with id= AZ, first strand: chain 'M' and resid 163 through 165 Processing sheet with id= BA, first strand: chain 'M' and resid 238 through 241 Processing sheet with id= BB, first strand: chain 'N' and resid 132 through 136 removed outlier: 6.576A pdb=" N THR N 103 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA N 135 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU N 105 " --> pdb=" O ALA N 135 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'N' and resid 35 through 38 Processing sheet with id= BD, first strand: chain 'N' and resid 163 through 165 Processing sheet with id= BE, first strand: chain 'N' and resid 238 through 241 Processing sheet with id= BF, first strand: chain 'O' and resid 132 through 136 removed outlier: 6.668A pdb=" N THR O 103 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA O 135 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU O 105 " --> pdb=" O ALA O 135 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'O' and resid 34 through 38 Processing sheet with id= BH, first strand: chain 'O' and resid 163 through 165 removed outlier: 3.517A pdb=" N VAL O 163 " --> pdb=" O VAL O 152 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'O' and resid 238 through 241 3120 hydrogen bonds defined for protein. 8781 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.00 Time building geometry restraints manager: 20.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 11024 1.31 - 1.44: 16372 1.44 - 1.58: 33667 1.58 - 1.72: 303 1.72 - 1.85: 655 Bond restraints: 62021 Sorted by residual: bond pdb=" CB HIS D 161 " pdb=" CG HIS D 161 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.99e+01 bond pdb=" SD MET S 8 " pdb=" CE MET S 8 " ideal model delta sigma weight residual 1.791 1.634 0.157 2.50e-02 1.60e+03 3.95e+01 bond pdb=" SD MET Z 8 " pdb=" CE MET Z 8 " ideal model delta sigma weight residual 1.791 1.634 0.157 2.50e-02 1.60e+03 3.94e+01 bond pdb=" CA ILE R 4 " pdb=" CB ILE R 4 " ideal model delta sigma weight residual 1.544 1.467 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" CA ILE Y 4 " pdb=" CB ILE Y 4 " ideal model delta sigma weight residual 1.544 1.467 0.077 1.26e-02 6.30e+03 3.75e+01 ... (remaining 62016 not shown) Histogram of bond angle deviations from ideal: 93.07 - 101.98: 321 101.98 - 110.89: 20603 110.89 - 119.80: 35894 119.80 - 128.71: 26595 128.71 - 137.62: 344 Bond angle restraints: 83757 Sorted by residual: angle pdb=" N VAL N 163 " pdb=" CA VAL N 163 " pdb=" C VAL N 163 " ideal model delta sigma weight residual 107.56 117.54 -9.98 9.10e-01 1.21e+00 1.20e+02 angle pdb=" C ALA N 331 " pdb=" N PRO N 332 " pdb=" CA PRO N 332 " ideal model delta sigma weight residual 119.66 126.93 -7.27 7.20e-01 1.93e+00 1.02e+02 angle pdb=" N VAL L 163 " pdb=" CA VAL L 163 " pdb=" C VAL L 163 " ideal model delta sigma weight residual 107.89 117.52 -9.63 1.09e+00 8.42e-01 7.81e+01 angle pdb=" C GLN C 263 " pdb=" N PRO C 264 " pdb=" CA PRO C 264 " ideal model delta sigma weight residual 119.82 128.24 -8.42 9.80e-01 1.04e+00 7.37e+01 angle pdb=" C GLN N 263 " pdb=" N PRO N 264 " pdb=" CA PRO N 264 " ideal model delta sigma weight residual 119.56 128.19 -8.63 1.02e+00 9.61e-01 7.16e+01 ... (remaining 83752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 37552 35.85 - 71.71: 510 71.71 - 107.56: 41 107.56 - 143.41: 15 143.41 - 179.26: 10 Dihedral angle restraints: 38128 sinusoidal: 15816 harmonic: 22312 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.74 179.26 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP M 401 " pdb=" O3A ADP M 401 " pdb=" PB ADP M 401 " pdb=" PA ADP M 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.14 -175.15 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.70 -172.71 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 38125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 6428 0.096 - 0.193: 2272 0.193 - 0.289: 483 0.289 - 0.385: 76 0.385 - 0.482: 14 Chirality restraints: 9273 Sorted by residual: chirality pdb=" C3' ADP M 401 " pdb=" C2' ADP M 401 " pdb=" C4' ADP M 401 " pdb=" O3' ADP M 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.99 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CB ILE R 4 " pdb=" CA ILE R 4 " pdb=" CG1 ILE R 4 " pdb=" CG2 ILE R 4 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CB ILE Y 4 " pdb=" CA ILE Y 4 " pdb=" CG1 ILE Y 4 " pdb=" CG2 ILE Y 4 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 9270 not shown) Planarity restraints: 10873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 401 " -0.530 2.00e-02 2.50e+03 2.14e-01 1.26e+03 pdb=" C2 ADP E 401 " 0.108 2.00e-02 2.50e+03 pdb=" C4 ADP E 401 " 0.120 2.00e-02 2.50e+03 pdb=" C5 ADP E 401 " 0.037 2.00e-02 2.50e+03 pdb=" C6 ADP E 401 " -0.077 2.00e-02 2.50e+03 pdb=" C8 ADP E 401 " 0.225 2.00e-02 2.50e+03 pdb=" N1 ADP E 401 " -0.022 2.00e-02 2.50e+03 pdb=" N3 ADP E 401 " 0.145 2.00e-02 2.50e+03 pdb=" N6 ADP E 401 " -0.282 2.00e-02 2.50e+03 pdb=" N7 ADP E 401 " 0.117 2.00e-02 2.50e+03 pdb=" N9 ADP E 401 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP J 401 " -0.508 2.00e-02 2.50e+03 2.02e-01 1.12e+03 pdb=" C2 ADP J 401 " 0.084 2.00e-02 2.50e+03 pdb=" C4 ADP J 401 " 0.133 2.00e-02 2.50e+03 pdb=" C5 ADP J 401 " 0.036 2.00e-02 2.50e+03 pdb=" C6 ADP J 401 " -0.072 2.00e-02 2.50e+03 pdb=" C8 ADP J 401 " 0.196 2.00e-02 2.50e+03 pdb=" N1 ADP J 401 " -0.038 2.00e-02 2.50e+03 pdb=" N3 ADP J 401 " 0.154 2.00e-02 2.50e+03 pdb=" N6 ADP J 401 " -0.245 2.00e-02 2.50e+03 pdb=" N7 ADP J 401 " 0.089 2.00e-02 2.50e+03 pdb=" N9 ADP J 401 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP I 401 " -0.481 2.00e-02 2.50e+03 1.91e-01 1.00e+03 pdb=" C2 ADP I 401 " 0.046 2.00e-02 2.50e+03 pdb=" C4 ADP I 401 " 0.148 2.00e-02 2.50e+03 pdb=" C5 ADP I 401 " 0.049 2.00e-02 2.50e+03 pdb=" C6 ADP I 401 " -0.058 2.00e-02 2.50e+03 pdb=" C8 ADP I 401 " 0.164 2.00e-02 2.50e+03 pdb=" N1 ADP I 401 " -0.050 2.00e-02 2.50e+03 pdb=" N3 ADP I 401 " 0.157 2.00e-02 2.50e+03 pdb=" N6 ADP I 401 " -0.222 2.00e-02 2.50e+03 pdb=" N7 ADP I 401 " 0.070 2.00e-02 2.50e+03 pdb=" N9 ADP I 401 " 0.177 2.00e-02 2.50e+03 ... (remaining 10870 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 9042 2.75 - 3.29: 64604 3.29 - 3.82: 106242 3.82 - 4.36: 143206 4.36 - 4.90: 219335 Nonbonded interactions: 542429 Sorted by model distance: nonbonded pdb=" NZ LYS X 268 " pdb=" OE1 GLU a 117 " model vdw 2.211 2.520 nonbonded pdb=" NZ LYS Q 268 " pdb=" OE1 GLU T 117 " model vdw 2.211 2.520 nonbonded pdb=" CG LYS M 213 " pdb=" OH TYR M 306 " model vdw 2.217 3.440 nonbonded pdb=" NZ LYS I 326 " pdb=" OD1 ASP Q 219 " model vdw 2.223 2.520 nonbonded pdb=" CB ASP F 25 " pdb=" O LEU U 144 " model vdw 2.232 3.440 ... (remaining 542424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'T' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'b' } ncs_group { reference = chain 'V' selection = chain 'c' } Set up NCS constraints Number of NCS constrained groups: 6 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' } pdb_interpretation.ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' } pdb_interpretation.ncs_group { reference = chain 'T' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'U' selection = chain 'b' } pdb_interpretation.ncs_group { reference = chain 'V' selection = chain 'c' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 4.210 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 123.160 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.700 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4426 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.157 62021 Z= 1.225 Angle : 1.813 21.372 83757 Z= 1.226 Chirality : 0.102 0.482 9273 Planarity : 0.011 0.214 10873 Dihedral : 12.391 179.264 23730 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.02 % Favored : 97.44 % Rotamer: Outliers : 0.41 % Allowed : 1.41 % Favored : 98.18 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.09), residues: 7607 helix: -0.67 (0.07), residues: 4083 sheet: 0.55 (0.20), residues: 650 loop : 0.83 (0.12), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.014 TRP N 340 HIS 0.021 0.002 HIS H 161 PHE 0.039 0.006 PHE V 156 TYR 0.114 0.009 TYR L 166 ARG 0.012 0.001 ARG O 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15214 Ramachandran restraints generated. 7607 Oldfield, 0 Emsley, 7607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15214 Ramachandran restraints generated. 7607 Oldfield, 0 Emsley, 7607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1365 time to fit residues: 7.2222 Evaluate side-chains 29 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2447 time to fit residues: 0.6367 Evaluate side-chains 9 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.209 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1222 time to fit residues: 1.5598 Evaluate side-chains 5 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2825 Evaluate side-chains 3 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0864 time to fit residues: 0.3037 Evaluate side-chains 3 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0322 Evaluate side-chains 2 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4340 time to fit residues: 1.0569 Evaluate side-chains 0 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1590 Evaluate side-chains 4 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2282 time to fit residues: 1.0915 Evaluate side-chains 2 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1285 Evaluate side-chains 13 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0785 time to fit residues: 1.3151 Evaluate side-chains 11 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 637 optimal weight: 7.9990 chunk 572 optimal weight: 3.9990 chunk 317 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 386 optimal weight: 7.9990 chunk 305 optimal weight: 8.9990 chunk 591 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 359 optimal weight: 0.9980 chunk 440 optimal weight: 0.9990 chunk 685 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 68 GLN ** Q 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 271 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 48 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 2.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.099 1.519 62021 Z= 6.360 Angle : 3.899 49.202 83757 Z= 2.338 Chirality : 0.230 2.730 9273 Planarity : 0.019 0.431 10873 Dihedral : 13.715 170.622 8514 Min Nonbonded Distance : 0.720 Molprobity Statistics. All-atom Clashscore : 189.41 Ramachandran Plot: Outliers : 6.93 % Allowed : 6.78 % Favored : 86.29 % Rotamer: Outliers : 7.46 % Allowed : 5.87 % Favored : 86.67 % Cbeta Deviations : 14.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.10), residues: 7607 helix: -1.66 (0.08), residues: 3737 sheet: 0.66 (0.19), residues: 810 loop : 0.10 (0.13), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP D 86 HIS 0.056 0.002 HIS Q 276 PHE 0.113 0.005 PHE T 248 TYR 0.138 0.006 TYR X 162 ARG 0.066 0.003 ARG U 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14444 Ramachandran restraints generated. 7222 Oldfield, 0 Emsley, 7222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14444 Ramachandran restraints generated. 7222 Oldfield, 0 Emsley, 7222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1451 time to fit residues: 8.1841 Evaluate side-chains 33 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3431 Evaluate side-chains 149 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 36 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 23 residues processed: 136 average time/residue: 0.1643 time to fit residues: 24.5921 Evaluate side-chains 47 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 24 time to evaluate : 0.206 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1032 time to fit residues: 2.9800 Evaluate side-chains 4 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 4 average time/residue: 0.0638 time to fit residues: 0.3021 Evaluate side-chains 3 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0324 Evaluate side-chains 8 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3 time to evaluate : 0.115 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 8 average time/residue: 0.1246 time to fit residues: 1.2293 Evaluate side-chains 1 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1478 Evaluate side-chains 3 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.096 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 3 average time/residue: 0.0724 time to fit residues: 0.3885 Evaluate side-chains 2 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.096 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1281 Evaluate side-chains 24 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 14 time to evaluate : 0.116 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 23 average time/residue: 0.1079 time to fit residues: 2.8649 Evaluate side-chains 11 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 381 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 570 optimal weight: 0.5980 chunk 466 optimal weight: 10.0000 chunk 189 optimal weight: 0.0270 chunk 686 optimal weight: 20.0000 chunk 742 optimal weight: 0.0060 chunk 611 optimal weight: 40.0000 chunk 681 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 551 optimal weight: 1.9990 overall best weight: 1.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 12 ASN ** K 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 93 GLN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 263 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4033 moved from start: 2.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.094 1.565 62021 Z= 5.997 Angle : 3.857 50.837 83757 Z= 2.274 Chirality : 0.239 2.925 9273 Planarity : 0.017 0.333 10873 Dihedral : 13.003 161.354 8514 Min Nonbonded Distance : 0.878 Molprobity Statistics. All-atom Clashscore : 192.40 Ramachandran Plot: Outliers : 7.15 % Allowed : 7.19 % Favored : 85.66 % Rotamer: Outliers : 7.46 % Allowed : 5.00 % Favored : 87.54 % Cbeta Deviations : 13.81 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.10), residues: 7607 helix: -1.52 (0.08), residues: 3562 sheet: 1.00 (0.19), residues: 675 loop : -0.78 (0.12), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP N 86 HIS 0.048 0.003 HIS Q 276 PHE 0.080 0.004 PHE a 248 TYR 0.155 0.009 TYR Q 261 ARG 0.044 0.003 ARG U 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14200 Ramachandran restraints generated. 7100 Oldfield, 0 Emsley, 7100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14200 Ramachandran restraints generated. 7100 Oldfield, 0 Emsley, 7100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.1287 time to fit residues: 6.6918 Evaluate side-chains 31 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3822 Evaluate side-chains 132 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 26 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 30 residues processed: 117 average time/residue: 0.1953 time to fit residues: 24.8744 Evaluate side-chains 49 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 19 time to evaluate : 0.203 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 2 residues processed: 30 average time/residue: 0.0801 time to fit residues: 3.1087 Evaluate side-chains 3 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0748 time to fit residues: 0.2689 Evaluate side-chains 3 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0317 Evaluate side-chains 9 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3 time to evaluate : 0.109 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 9 average time/residue: 0.2171 time to fit residues: 2.1882 Evaluate side-chains 2 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0137 time to fit residues: 0.1674 Evaluate side-chains 5 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3 time to evaluate : 0.093 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 5 average time/residue: 0.0688 time to fit residues: 0.5245 Evaluate side-chains 2 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1253 Evaluate side-chains 21 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 12 time to evaluate : 0.114 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 20 average time/residue: 0.1127 time to fit residues: 2.6013 Evaluate side-chains 11 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 678 optimal weight: 0.9980 chunk 516 optimal weight: 0.9980 chunk 356 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 327 optimal weight: 0.9990 chunk 461 optimal weight: 20.0000 chunk 689 optimal weight: 10.0000 chunk 729 optimal weight: 20.0000 chunk 360 optimal weight: 5.9990 chunk 653 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 130 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3909 moved from start: 2.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.090 1.447 62021 Z= 5.786 Angle : 3.989 54.489 83757 Z= 2.319 Chirality : 0.244 2.275 9273 Planarity : 0.019 0.354 10873 Dihedral : 12.593 156.122 8514 Min Nonbonded Distance : 0.978 Molprobity Statistics. All-atom Clashscore : 199.45 Ramachandran Plot: Outliers : 7.76 % Allowed : 6.90 % Favored : 85.34 % Rotamer: Outliers : 6.48 % Allowed : 3.91 % Favored : 89.61 % Cbeta Deviations : 13.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.09), residues: 7607 helix: -1.95 (0.08), residues: 3570 sheet: 0.80 (0.18), residues: 675 loop : -1.27 (0.11), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP O 86 HIS 0.031 0.002 HIS P 276 PHE 0.112 0.006 PHE c 104 TYR 0.226 0.010 TYR W 221 ARG 0.081 0.003 ARG U 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14200 Ramachandran restraints generated. 7100 Oldfield, 0 Emsley, 7100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14200 Ramachandran restraints generated. 7100 Oldfield, 0 Emsley, 7100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0948 time to fit residues: 4.6646 Evaluate side-chains 30 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3427 Evaluate side-chains 126 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 26 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 35 residues processed: 113 average time/residue: 0.1809 time to fit residues: 22.4286 Evaluate side-chains 56 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 21 time to evaluate : 0.203 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 2 residues processed: 35 average time/residue: 0.0863 time to fit residues: 3.8114 Evaluate side-chains 4 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 3 average time/residue: 0.0769 time to fit residues: 0.2763 Evaluate side-chains 3 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0321 Evaluate side-chains 4 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1 time to evaluate : 0.108 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 4 average time/residue: 0.2626 time to fit residues: 1.2508 Evaluate side-chains 0 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1479 Evaluate side-chains 3 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.094 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 3 average time/residue: 0.0673 time to fit residues: 0.3836 Evaluate side-chains 2 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1273 Evaluate side-chains 17 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 11 time to evaluate : 0.115 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 16 average time/residue: 0.0991 time to fit residues: 1.9017 Evaluate side-chains 11 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 607 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 543 optimal weight: 20.0000 chunk 301 optimal weight: 0.0570 chunk 622 optimal weight: 1.9990 chunk 504 optimal weight: 9.9990 chunk 0 optimal weight: 0.0970 chunk 372 optimal weight: 50.0000 chunk 655 optimal weight: 50.0000 chunk 184 optimal weight: 0.8980 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 68 GLN P 93 GLN P 202 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 266 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3755 moved from start: 2.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 1.317 62021 Z= 5.335 Angle : 4.059 60.655 83757 Z= 2.325 Chirality : 0.238 2.202 9273 Planarity : 0.019 0.262 10873 Dihedral : 12.455 178.170 8514 Min Nonbonded Distance : 0.929 Molprobity Statistics. All-atom Clashscore : 202.53 Ramachandran Plot: Outliers : 7.91 % Allowed : 7.95 % Favored : 84.13 % Rotamer: Outliers : 5.29 % Allowed : 5.63 % Favored : 89.09 % Cbeta Deviations : 13.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.09), residues: 7607 helix: -2.18 (0.08), residues: 3546 sheet: -0.31 (0.22), residues: 435 loop : -1.32 (0.11), residues: 3626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP O 86 HIS 0.063 0.003 HIS Q 276 PHE 0.093 0.006 PHE c 101 TYR 0.136 0.008 TYR X 214 ARG 0.091 0.003 ARG W 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12852 Ramachandran restraints generated. 6426 Oldfield, 0 Emsley, 6426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12852 Ramachandran restraints generated. 6426 Oldfield, 0 Emsley, 6426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.268 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0965 time to fit residues: 4.4346 Evaluate side-chains 26 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3459 Evaluate side-chains 109 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 26 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 22 residues processed: 100 average time/residue: 0.1887 time to fit residues: 20.7080 Evaluate side-chains 39 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 17 time to evaluate : 0.201 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.0738 time to fit residues: 2.2213 Evaluate side-chains 7 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.024 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1835 time to fit residues: 1.3388 Evaluate side-chains 5 residues out of total 25 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0318 Evaluate side-chains 3 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1 time to evaluate : 0.109 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4786 time to fit residues: 1.1469 Evaluate side-chains 0 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1475 Evaluate side-chains 3 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.096 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 3 average time/residue: 0.2736 time to fit residues: 0.9926 Evaluate side-chains 3 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.095 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3416 time to fit residues: 0.4767 Evaluate side-chains 16 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.115 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 15 average time/residue: 0.0784 time to fit residues: 1.4853 Evaluate side-chains 12 residues out of total 141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.115 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0150 time to fit residues: 0.1758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.1319 > 50: distance: 0 - 1: 7.323 distance: 0 - 6: 31.527 distance: 1 - 2: 18.877 distance: 1 - 4: 62.750 distance: 2 - 3: 29.748 distance: 2 - 7: 21.674 distance: 5 - 6: 56.586 distance: 7 - 8: 18.318 distance: 8 - 9: 25.573 distance: 8 - 11: 18.178 distance: 9 - 10: 8.596 distance: 9 - 12: 38.856 distance: 12 - 13: 40.441 distance: 13 - 14: 16.886 distance: 13 - 16: 43.042 distance: 14 - 15: 22.471 distance: 14 - 20: 25.111 distance: 16 - 17: 38.891 distance: 17 - 18: 45.158 distance: 18 - 19: 11.252 distance: 20 - 21: 12.735 distance: 21 - 22: 19.322 distance: 21 - 24: 43.058 distance: 22 - 23: 24.347 distance: 22 - 32: 21.268 distance: 25 - 26: 39.852 distance: 25 - 27: 4.162 distance: 26 - 28: 20.678 distance: 27 - 29: 11.935 distance: 28 - 30: 17.974 distance: 29 - 30: 35.084 distance: 30 - 31: 30.104 distance: 32 - 33: 35.623 distance: 33 - 34: 35.133 distance: 33 - 36: 25.615 distance: 34 - 35: 5.491 distance: 34 - 39: 34.689 distance: 36 - 37: 42.040 distance: 36 - 38: 41.479 distance: 39 - 40: 11.818 distance: 40 - 41: 17.764 distance: 40 - 43: 29.802 distance: 41 - 42: 15.153 distance: 41 - 44: 43.128 distance: 44 - 45: 18.578 distance: 45 - 46: 41.105 distance: 45 - 48: 17.042 distance: 46 - 47: 21.340 distance: 46 - 52: 38.614 distance: 48 - 50: 25.276 distance: 49 - 51: 13.678 distance: 52 - 53: 16.333 distance: 53 - 54: 30.739 distance: 53 - 56: 3.485 distance: 54 - 55: 16.545 distance: 54 - 61: 30.922 distance: 56 - 57: 3.207 distance: 57 - 58: 12.046 distance: 58 - 59: 22.824 distance: 58 - 60: 11.408 distance: 61 - 62: 36.745 distance: 62 - 63: 21.958 distance: 62 - 65: 18.978 distance: 63 - 64: 25.006 distance: 63 - 66: 35.845 distance: 66 - 67: 16.084 distance: 67 - 68: 4.834 distance: 67 - 70: 17.479 distance: 68 - 69: 20.854 distance: 70 - 71: 21.707 distance: 70 - 72: 24.693